Contacts of the strand formed by residues 214 - 222 (chain C) in PDB entry 6VSU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C PRO* 3.9 6.0 - - - +
179C VAL 2.7 16.6 - - - +
181C ILE* 3.7 26.9 - - + -
208C ILE* 3.9 6.2 + - + +
209C MET* 3.8 34.0 - - + +
212C GLY* 3.9 13.2 - - - -
213C TYR* 1.3 76.9 - - - +
215C ARG* 1.3 60.2 + - - +
216C ARG 5.1 2.7 - - - +
217C LEU* 5.3 0.9 - - + +
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C PRO* 4.0 8.0 - - + +
179C VAL 3.0 8.3 + - - -
180C ASP* 2.9 28.0 + - - +
209C MET* 3.7 14.4 - - - +
214C ALA* 1.3 72.1 - - - +
216C ARG* 1.3 74.5 + - + +
217C LEU 3.6 2.4 + - - -
236C PHE 4.9 3.8 - - - +
237C GLY 5.0 3.3 - - - +
260C GLU 2.3 38.8 + - - +
261C GLY* 4.1 9.3 + - - -
262C VAL* 3.0 42.1 - - + +
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Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP* 2.8 36.9 + - + +
181C ILE* 2.7 34.2 + - - +
214C ALA* 5.2 1.3 - - - -
215C ARG* 1.3 88.8 - - + +
217C LEU* 1.3 53.3 + - - +
218C LEU* 3.7 13.4 - - + +
239C GLU* 2.7 44.6 + - - +
252C MET* 5.6 7.9 - - - +
256C LEU* 5.7 1.0 - - - +
257C LYS 3.7 12.3 + - - -
258C LEU* 3.5 21.7 - - + +
259C GLY 5.4 0.2 - - - +
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 3.5 36.3 - - + +
183C HIS* 4.0 10.5 - - + -
190C ILE* 4.9 2.0 - - + -
205C PHE* 3.6 32.3 - - + -
209C MET* 4.1 27.6 - - + -
214C ALA* 5.3 0.9 - - + +
215C ARG 3.6 4.4 + - - -
216C ARG* 1.3 69.4 - - - +
218C LEU* 1.4 56.8 + - - +
219C GLN* 3.5 26.7 - - + +
237C GLY 5.2 3.4 + - - -
238C VAL* 3.1 28.6 - - + +
239C GLU* 2.9 30.2 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ILE 3.0 12.2 + - - +
182C LEU* 3.6 12.0 - - + +
183C HIS* 2.9 32.0 + - - +
216C ARG* 3.7 9.0 - - + +
217C LEU* 1.4 70.3 - - - +
219C GLN* 1.3 57.8 + - - +
220C VAL* 4.4 3.4 - - + -
239C GLU* 3.2 47.8 - - + +
241C TYR* 4.3 10.5 - - + +
256C LEU* 3.5 41.7 - - + -
258C LEU* 3.6 33.2 - - + -
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Residues in contact with GLN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C HIS* 2.9 29.5 + - - +
188C PRO* 2.8 35.5 + - - +
190C ILE* 4.6 3.3 - - - +
205C PHE* 4.3 1.6 - - - +
217C LEU* 3.5 19.6 - - + +
218C LEU* 1.3 73.5 - - - +
220C VAL* 1.3 57.4 + - - +
222C ILE* 4.0 18.1 - - + +
238C VAL* 3.4 19.6 - - + +
239C GLU 3.0 6.1 + - - +
240C GLN* 3.2 37.2 + - - +
241C TYR* 2.7 35.0 + - - +
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LEU* 3.7 23.6 - - + -
183C HIS 2.9 6.6 + - - +
184C LEU* 3.3 28.8 - - + +
185C ASP 3.0 24.0 + - - -
218C LEU* 4.3 4.3 - - + +
219C GLN* 1.3 78.0 - - - +
221C GLY* 1.3 64.0 + - - +
222C ILE* 3.3 1.9 - - - +
241C TYR* 3.8 9.9 - - + -
246C PHE* 5.4 0.4 - - + -
253C LEU* 3.9 40.4 - - + -
256C LEU* 4.8 2.5 - - + -
273C CYS* 4.5 0.7 - - - +
290C LEU* 4.6 5.2 - - + -
298C ILE* 4.1 15.5 - - + -
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Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ASP 3.1 11.5 - - - +
186C ALA* 3.4 1.7 - - - -
220C VAL* 1.3 75.4 - - - +
222C ILE* 1.4 64.2 + - - +
223C ARG* 2.8 28.0 + - - -
241C TYR* 3.5 4.9 + - - +
243C MET* 3.6 26.0 - - - +
246C PHE* 6.1 0.2 - - - -
253C LEU* 5.8 0.4 - - - +
273C CYS 4.8 0.7 - - - -
290C LEU* 4.1 13.7 - - - -
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C HIS* 5.6 0.2 - - + -
185C ASP* 3.5 7.2 - - + +
186C ALA 3.4 5.2 - - - +
187C HIS 3.0 36.3 - - - +
188C PRO* 3.6 12.3 - - + -
219C GLN* 4.0 27.8 - - + +
221C GLY* 1.4 75.7 - - - +
223C ARG* 1.3 59.5 + - - +
224C SER 4.6 0.4 - - - +
225C ILE* 4.1 28.9 - - + -
240C GLN* 4.9 5.4 - - + -
241C TYR 3.3 18.5 + - - +
242C GLU* 3.0 23.4 - - + +
243C MET 2.7 32.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il